(Afther change “,” for “tab” …)Content in MAF format Tumor_Seq_Allele1 and Tumor_Seq_Allele2, why your data only use Ref_seq or only have Tumor_Seq_Allele1.
How could correct this ?? copy the column two times?? All MAF programs use this column…
Hi. I suspect that the four columns that you are referring to are due to presence of matched normal in some other somatic MAF files (e.g. TCGA). We do not have/use matched normal samples, so we only report two columns related to the reference genome and the tumor allele.
Ok, but the somatic mutations from cell lines will be homozygous and heterozygous. Alle1/alle2. Supouse are heterozygous? (The other allele equal to reference).
No, these two columns are reference and alternate alleles regardless of zygosity. This file does not have zygosity information directly, but you can use the counts in CGA_WES_AC column to extract the number of reference/alternate alleles
